The Flare War
by Culius Jaesar
Summary: A reboot of the fight against Team Flare, where Lysandre manages to enslave the Zygarde 'Complete Forme' and wreak havoc across Lumiose City, while Ash, Serena and the best Kalos has to offer try to stop him, before it's too late. Mild Amourshipping.


The Flare War had devastated Lumiose City. Horde after horde of Grunts had plagued it, being repelled only after the Gym Leaders and Pokemon League Trainers had joined hands to do so. However, Lysandre, in the meantime, had harnessed power far beyond anyone's imagination; the power to enslave a Legendary Pokemon.

The orange haired man had used this power on one of the Zygarde Cores, code-named Z2, to purge all the goodness and order from its heart. Now, only chaos remained.

The other Zygarde Core, code-named Z1, nicknamed Squishy, had transformed into its 50% form to fight its other. The battle had wrought destruction only Legendary Pokemon could be capable of. The two were equal in might, speed, longevity, everything. But Squishy hesitated to use its full power. How could it? It was fighting its other, after all. It was akin to fighting a twin brother. Z2, controlled as it was, took advantage of this hesitance to overwhelm Squishy, and bring it under Lysandre's control as well.

Just as he had wanted. Without wasting any time, Lysandre forced the two cores to merge, Power Construct activating and liberating the Zygarde "Complete Forme". Now, there was little to nothing that could stop it. The Order Pokemon wreaked havoc on Lumiose under Lysandre's unfaltering command, and reduced the proud capital city of Kalos to a mere husk of itself. Basalt rubble, glass, metal, broken piping, porcelain, everything, covered the earth. Even the sky high Prism Tower had been completely fragmented, split into innumerable pieces of steel, glass, and Arceus knew what else. Blackish-red roots had erupted from the ground under Zygarde's influence to cause further disarray.

The Trainers that had fought Zygarde along with the Gym Leaders had all either fled the city, or stayed to fight. The latter half had been nearly decimated by the roots, or by the Flare Grunts, especially Bryony, Celosia and Xerosic. Eventually, they were all defeated; Bryony by Clemont and his faithful Luxray, Celosia by the celebrated hero Blaziken Mask, and Xerosic by the combined efforts of Serena's Braixen and Mairin's Chespin. Despite only a handful of trainers remaining, they believed; _we can win_.

How wrong they were. Zygarde chased them all off with ease, either by raining green arrows upon them or by blasting them back with green hexagons generated from its body. Now only one trainer and two of his Pokemon remained still healthy enough to fight. These two Pokemon were Greninja; as in Ash-Greninja, and Pikachu. These raced up and down the titanic Order Pokemon, either hitting it with Aerial Ace and Iron Tail respectively, or pulling back and using Quick Attack and Water Shuriken to deal some minuscule damage to Zygarde's arms. It was barely working. Zygarde was near indestructible. The ninja frog and mouse could hardly dodge its arrows or sneak past its arms. There was little to no hope for any of them.

The remainder of the Trainers and Gym Leaders huddled together behind a pile of rubble. The majority looked lost, broken. They were unknowing of what to do. Serena, Clemont, Bonnie, Astrid, Korrina, Sawyer, Alain, Grant, Wulfric, Blaziken Mask, Steven Stone and a few others were among the majorly uninjured. Many more, including the Champion and Elite Four were piled in the miraculously still-undamaged Pokemon Centre.

Serena looked worriedly at the black haired boy, who was at a safe distance away from her, and the two blurs attacking Zygarde futilely. She loved him and was fearful of what the next few minutes could bring about. His death? Hers? Everybody else's?

"Sit down, Serena," came a voice. Grant's voice.

The honey blonde stared defiantly at the dark-skinned Gym Leader. "No."

"Listen to me, I have a plan," stated Grant, ignoring her. Serena acquiesced to his demand after a few moments of defiance, paying heed to Grant's eyes. They were red-rimmed, obviously because of a certain pretty Santalune City Gym Leader being in critical condition with a punctured lung, broken leg and what else...

"In a matter of a few minutes, we are all going to die," claimed the dark-skinned Gym Leader bluntly, breaking Serena out of her reverie.

"Not if Ash wins we won't," countered Korrina. She was leaning heavily on Clemont, her Lucario by her side. Grant glared at her. "We all know that there is no chance of that happening." Everyone hissed at those words. They were true, after all.

"What do you propose we do, then?" asked Clemont hesitantly, "you said you had a plan."

"Yes," agreed Grant, pulling out a stoppered vial filled with blue liquid and holding it up. "This is a Super Potion. One drop of it can cure a Pokemon of all its injuries, and this has enough to cure about ten Pokemon. Wulfric has one of these too...and Sawyer's Clawitzer, if I'm not wrong, knows Heal Pulse. So, with our combined efforts, we'll be able to heal about thirty Pokemon, enough to mount a major assault on Zygarde and Lysandre once more."

There was a silence, and then, "That's brilliant!" shouted Korrina over the sudden murmuring that had occurred throughout the horde of trainers. "Let's start now."

"Hold, hold!" called Wulfric, silencing the Trainers. "We shall need to discuss a plan first, so we can, y'know...fight Zygarde conclusively. We can't fight it with a, y'know, half thought-out plan, so we need to think this through carefully."

"Wulfric is right." Grant was calm as he handed out the Potion to everyone. "Squeeze out a drop of this in your Pokemon's mouths, while we detail out a plan."

While the healing process occurred, Sawyer's Howitzer Pokemon joining in by letting out a pinkish-white wave with a mother-of-pearl sheen to it, Steven, Grant, Wulfric and even Blaziken Mask tried to concur on a single strategy, which didn't take long. The final plan was simple, nine Trainers, preferably Alain, Clemont, Sawyer, Astrid, and the adults being among them, would go upfront to assist Ash in directly attacking Zygarde (cause Arceus knew he would run out of steam sooner or later; most likely the former). Less powerful trainers would focus on maintaining support with ranged attacks and healing moves like Wish and Heal Pulse.

"Seems a simple plan," stated Clemont, adjusting his glasses, "perhaps a bit _too_ simple for taking down a Legendary?"

"Simple is how we're supposed to roll, inventor boy," scoffed Korrina jokingly.

Serena's worry did not alleviate just yet. The probability of anyone of them being killed was high. And yet, her gut instinct told her that this was the best chance they had.

"Okay!" called Steven when the healing had finished. Several Pokemon were now looking healthy and ready to fight. Serena noticed that several Trainers had already called out their other Pokemon (that they hadn't used yet), so she did as well, her Braixen and Sylveon landing neatly on the ground. Metagross glittered as Steven Mega-Evolved it, its claws sharpened and mind alert. Bonnie wished her brother luck, clasping his hand with a tearful expression. "Plan commence!"

As planned, Alain, Clemont, Korrina, Sawyer, Blaziken Mask, Astrid, Steven, Serena herself and a boy they did not know sprinted toward Zygarde, close enough to hear Lysandre's horrible laughter echo everywhere throughout Lumiose City from his perch on top of a still-intact tower. "Give up, boy, there is no way you can stand up to a Legendary Pokemon!"

"Not today!" was the brave reply, "use Quick Attack and Cut!"

"Ninja!" Greninja drew the silvery shining sword from his back and swiped furiously at the titan's chest that resembled a face. Pikachu cried valiantly, rocketing into Zygarde's knee with a white aura whipping around him, but it did nothing. Could do nothing.

"I'm gonna take you down for sure!" Ash sounded confident, but it didn't take a genius to tell that he was getting desperate. His Pokemon were becoming winded and Zygarde had barely suffered any damage.

"Braixen, use Fire Blast!" yelled Serena. The Fox Pokemon nodded, a five-pronged blast of flame emerging from her wand to hit Zygarde on the head. Ash spun around to see who'd done that, his eyes lighting up in horror when he did. "What on earth are you doing here!? Get back! I'll handle Zygarde myself!"

"Not for long you won't," asserted Steven sternly. "Metagross, please use Meteor Mash!"

"Meh taaa!" the Iron Leg Pokemon shot towards Zygarde with a solid blue aura coalescing around it to slam its chest. The Order Pokemon shuddered slightly, only to call upon its green arrows once more to rain on Metagross, who could thankfully evade most of them. Ash just stared slack-jawed. "Why?" he mumbled.

"Because we'd rather you didn't die," scoffed the unknown boy, sending out a Trevenant. "Energy Ball!"

"Trev!" An insane number of Energy Balls gathered around Trevenant's body before speeding over to intercept the flying arrows coming for them. Astrid peered at him while calling out her Absol. "Hey...what's your name?" She sounded impressed by his strength.

"Jack," the boy answered succinctly. He had silver, messy hair, grey eyes and wore a grey jacket with sleeves rolled up till between his elbows and wrists, along with dark blue jeans and black leather sandals. He was a little shorter than Astrid, yet carried himself with pride and dignity. "Now, Trevenant, Phantom Force."

The Elder Tree Pokemon disappeared suddenly, only to reappear behind Zygarde to swipe at it. Astrid took advantage of this momentary distraction, as did Serena, Clemont and the others.

"Absol, use Dark Pulse!" Absol screamed loudly before blasting out a dark purple helix from his mouth which did nothing but further aggrieve Zygarde. However, a Water Shuriken from Greninja, Flamethrower from Blaziken, Swift from Luxray, Fairy Wind from Sylveon, Blast Burn from Charizard, and Leaf Storm from Sceptile soon followed, nearly bringing the titan to its knees, even if it looked more annoyed than hurt.

"Mega Evolve, Sceptile!" cried Sawyer, "and use Frenzy Plant!"

"Scep...tiiiile!" the Forest Pokemon screeched hoarsely, sending up some thick, dark green roots to stab at Zygarde's chest. Mega Charizard followed soon after, its Blast Burn ripping apart the earth and covering the Order Pokemon with a maelstrom of blue fire.

"Not bad, not bad..." tutted Lysandre, "however, it's not enough, nor will it ever be. A thousand waves shall push you backward, and a thousand arrows shall annihilate you! Now, Zygarde!"

"Not today, use Aura Sphere!" roared Korrina. Mega Lucario grunted and threw the pearlescent blue sphere at Zygarde who merely batted it aside and fired a gigantic rainbow-like beam from its chest's 'mouth'. Everybody shouted in alarm, ordering their Pokemon to use Protect, or anything to defend them. The support team did so in time, a green shield coming up to block the beam. However, the beam did nothing to them, merely striking the ground underneath them and scarring it with a green Z-shaped mark. Nothing happened for a moment and all the Trainers decided to attack Zygarde once more, but-

" _Everyone, watch out!_ " Jack shrieked, and called his Trevenant over to the shield. "Phantom Force, get us away from the Z!" The jade, cosmic lettering had started to glow dangerously.

"Trevenant!" it cried, holding up its claws while spreading its shadows all around to teleport them away from the earth...just as it exploded. However, all were safe, the Elder Tree Pokemon having transported them away from the affected area.

"What..." said Steven. "How did you know to do that?!"

"Core Enforcer," explained Jack breathlessly. "That...is Zygarde's special signature move that blows up anything it touches...and what's more, any Pokemon that gets hit with it won't be able to use its Ability anymore...got that from one of the books stored in the Lumiose Library."

Thanking Jack for his quick action, everyone was now fired up to continue the assault, none more so than Ash. His Greninja and Pikachu were both complete wrecks, yet they were willing to fight along with everyone else, to save Kalos from its ruination.

Soon, Wishes and Heal Pulses started to arrive from the support team, healing most of the front line Pokemon before the mother of pearl glows petered out. Ash's two warriors, now recovered, started to determinedly besiege Zygarde once more, striking it with Water Shuriken and Iron Tail before being pushed back by the titan's green hexagons (Thousand Waves, identified Jack) and expertly landing on their feet uninjured.

"Heh heh," gurgled Lysandre. "I applaud you all for giving Zygarde such a bothersome fight. But, you know, don't you, Steven Stone? That you cannot win like this?!"

"Tch...Meteor Mash!" screamed Steven as his temper slipped from his grasp. Metagross growled, swooping on the Order Pokemon like a falling meteor. Zygarde barely flinched, striking Metagross away like it was nothing but an annoyance...which it probably was.

Jack cursed lowly, "Trevenant, Phantom Force to catch it."

The ghostly tree merely nodded before disappearing to catch the Iron Leg Pokemon with its strong claws. The azure haired man peered at his Pokemon to ensure it was safe, before whipping around to address the crowd.

"Lysandre is right," he claimed, which shocked Serena. She had believed that this man would be able to liberate Lumiose of this horrific power, but now here he was, declaring that they had little chance of winning. "This isn't enough...we need at least one more Mega Evolution to clinch this. Zygarde is hardly paying attention to any of our attacks. We have no chance of beating it at this rate."

"So how will one more Mega Evolution make a difference?" asked Sawyer sullenly. Serena agreed. If six Mega Evolved Pokemon, along with Ash-Greninja, his Pikachu, Jack's Trevenant, her own Braixen and Sylveon, and Clemont's Luxray couldn't beat Zygarde, then what difference would one more Pokemon make? Even now, Korrina, Blaziken Mask and Clemont's Pokemon were being defeated, shot down by 'Thousand Arrows', Jack had identified its green projectiles as.

"When I say a Mega Evolution, I mean one belonging to a trainer that is of my own calibre, and knows an Ice-type move or is a Ice-type- which would be extremely effective against Zygarde," explained Steven. "Possibly if that Jack person has a Mega Evolution Pokemon, then maybe..."

The said man wasn't really listening, holding back Zygarde with his Trevenant's innumerable Energy Balls that rained upon it like a conglomerate of pearlescent meteors. Ash was helping, his Greninja drawing out several Water Shurikens to assault Zygarde's face. These two seemed to be the only ones that were really annoying Zygarde, the titan roaring as it discharged a manifold of jade projectiles that Trevenant and Greninja dodged with Phantom Force and Aerial Ace respectively.

"Not enough," growled Jack. He snapped out another Pokeball, bursting out to reveal a mighty Swampert, surprising the Trainers. It looked healthy and did not seem to be wounded anywhere, showing that Jack had probably not used it in the League. "Rain Dance!"

"Swam!" it croaked, holding up its arms which were like battering rams to call upon thick cumulonimbus clouds that drenched the Pokemon in showers of rain. Braixen and the other Fire-types in the support team started complaining, so Serena and the others recalled them. She kept Sylveon out, however.

"Excellent, the rain will obstruct Zygarde's vision!" bayed Steven. "Now's our chance! Flash Cannon!"

Serena, Sawyer, and Astrid, along with their Pokemon were quick to react, sending out Fairy Wind, Leaf Storm and Psycho Cut respectively. These came upon and battered the titan, who could not counter, opting instead to try and wipe the rain away from its face. Alain and Charizard were moving a lot more slowly, but soon, the Flame Pokemon jetted down upon Zygarde to impale it with a super effective Dragon Claw. Zygarde, for the first time, grunted with pain and tried in vain to somehow slam Charizard down with its Thousand Waves attack. The black Dragon-type was unyielding whatsoever, swiping at the Order Pokemon with his sickly green claws once more.

"Absol, use Shadow Claw to assist!" yelled Astrid, the Disaster Pokemon complying as he slashed at Zygarde's leg with claws overflowing with shadows. "I'll support you guys! Serena, have Sylveon use any Fairy type move it can to clinch this! Alain, you too, with Charizard's Dragon-type moves!"

"Gotcha! Charizard, Dragon Claw!" roared Alain.

"Sylveon, use Fairy Wind!"

Ash joined in soon. "Greninja, use Water Shuriken!"

Pikachu had recently fallen to one of Zygarde's super effective Thousand Waves, and the Ninja Pokemon was furious and eager to avenge his brother-in-arms. The colossal shuriken on his back, now amplified by the recent Rain Dance, was once more, pitched at the titan with speed and power unparalleled; that is unparalleled by any Pokemon other than Zygarde itself. It collided with the Order Pokemon's face like a battering ram, Zygarde groaning at the pain.

"Time to finish this!" The groan that Zygarde had emitted had not gone unnoticed by the silver haired trainer; in a flash, his hand had swept up to his neck to clasp a shining pendant hanging from it. "Go, Mega Evolution!"

"Swaaaammpeeerrt!" the Mud Fish Pokemon screeched hoarsely, glowing with a multicoloured aura while its already gargantuan arms bloated significantly, now being clad with muscles that would put a Conkeldurr to shame, astonishing the coterie of trainers all around. Its hind legs grew exponentially shorter, gills erupting from its back. Even Lysandre broke off his deranged tirade to squint at the Mega Evolution. Once it finished, Jack ordered, "Earth Power!"

With a grunt, Swampert punched the ground, yellow cracks spreading through it and an ochre energy expelling from the cracks to blow up in Zygarde's face. Nobody hesitated to follow up.

"Charizard, let's get stronger together! Use Steel Wing!" ordered Alain firmly. Ash simply nodded at his faithful Greninja, who nodded back and leaped up to join the Flame Pokemon's assault with a silver sword sharp as steel in hand. Both Cut and Steel Wing failed to impact with Zygarde, however, which pushed them back with Thousand Waves.

The rain slowly began to peter out, which did not escape Jack's notice. "Swampert, Rain Dance once more, then use Waterfall."

"Pert!" it called, sweeping up its hands to summon the rain once more, before covering itself in a swirl of water and flying up at Zygarde with surprising speed. Obviously, Swampert's Swift Swim Ability had kicked in, increasing its speed to sky high levels, and Waterfall being stronger because of the rain. It was a perfect combo, making Mega Swampert a huge force to contend with.

"Don't let up, use Ice Punch!" roared the silver haired trainer, the Mud Fish Pokemon roaring along with him as it started to pummel Zygarde with everything it had. These apparently really affected Zygarde, the Order Pokemon howling in pain. "Now, if we can just release it from Lysandre's hold..."

Serena gasped. She understood it now. The whole point of this battle was _not_ to defeat Zygarde, but to save it from Team Flare's control. She almost felt a twinge of pity for the Order Pokemon that she hadn't been able to before, what with the fear and anger swirling about in her heart. But now...Lysandre's hold over it was too strong. The only hope they had now was to defeat Zygarde, and the only Pokemon that she considered strong enough to do that were Metagross, Swampert, Charizard, and of course, Greninja.

The said four were continually attacking the titan with every drop of power and passion they possessed. Charizard, his crimson eyes burning blue, unleashed a maelstrom of azure fire that flared up against Zygarde. Swampert, now on the ground once more, sent up another Earth Power at the Order Pokemon's back. Metagross, unyielding, was struggling to redirect Zygarde's arrows with Psychic, and Greninja, strikingly resembling the man she probably loved, running up and down Zygarde's back while driving Cut and Aerial Ace at its body.

It was inevitable. Zygarde was slowing, despite having long since knocked Clemont, Blaziken Mask, and Korrina out of the fight. Trevenant and Sceptile had been recalled into their Pokeballs, Sawyer having retreated from the fight a while ago. Her Sylveon was helping out along with Astrid's Absol, by sending out Swifts (or Fairy Winds) and Psycho Cuts respectively, and on occasion darting in to use Shadow Claw and Megahorn in Astrid's case.

"We'll get even, EVEN stronger!" screamed Ash. "One last attack, everybody! Let's make it a good one!"

"You got it! Charizard, use Blast Burn! Show this guy our true power!" roared Alain.

"Rawwwr!" the Flame Pokemon released its final maelstrom of blue flames, ripping apart the earth only to blast at Zygarde's chest.

"Let's show them a Champion's strength, Metagross!" The normally cultured, dignified Steven Stone was now screaming his heart out, raw passion overflowing out of his body. "Meteor Mash!"

"Mehtaaaaa!" Metagross caterwauled, streaking at the titan with its own titanic strength, a solid cerulean aura whipping around it. The Order Pokemon stumbled back, shocking Lysandre to the point where he started to command Zygarde to use Thousand Waves, Thousand Arrows, Core Enforcer, anything, but no use. Zygarde was on its last legs. A few more good hits would finish it.

"Swampert, I believe in you!" Jack was smiling widely for the first time, clenching his fists and punching the air with them. "One last Waterfall!"

Swampert nodded and raced up to the titan with swirls of water encompassing its whole body, leaping up to plough against the titan's chin, driving it up as the Mud Fish Pokemon landed proudly, although quite tired. Now, Zygarde's neck was exposed for Ash to freely aim at with all of Greninja's might.

"Greninja, this is our power!" howled Ash, Greninja taking to the air. "For everyone's sake, for Kalos' sake, one last _Water Shuriken!_ "

"Ninjaaa!"the Ninja Pokemon roared, the shuriken spinning as it impacted with Zygarde's neck, bringing it down with a resounding CRASH. It split into innumerable green cells that scattered everywhere, finally free from Lysandre's control. The said flame-haired man was howling, stupefied at Zygarde's defeat before Jack went up the tower he was on top of to kick him in the head and restrain him with a little help from Trevenant.

Peace had finally been restored to Kalos. Serena could feel happy tears sting her eyes. Every trainer, even Steven, was crying in joy, embracing all their comrades, their brothers and sister-in-arms that had fought with them to liberate Kalos from the menace of a Legendary. Lysandre, the madman that had masterminded this entire operation, was now safely in the hands of a few Officer Jenny that hadn't been too massively injured. Even in the hospital, the amalgamation of trainers were celebrating loudly and happily. Serena went up, running as fast as she could, to embrace the raven haired man that held her heart tightly.

Ash chuckled in a gravelly sort of voice, hugging her back as Greninja gently picked up Pikachu from the ground. "Hey, Serena...we won, right?"

"Yeah," she sniffled, tears wetting his jacket. "We won, Ash. We all did; you, me, Jack, Alain, Sawyer, everyone..."

"That's awesome," he croaked further. Serena let go of him to wipe the water from her eyes, only to start chuckling in amusement when Astrid enfolded Jack in her arms and the silver haired trainer screamed at her to "Let me _go_ , dammit!" only for Astrid to squeeze him harder.

Kalos had finally been freed. The Flare War was finally over.

* * *

 **Whoa, I had a lot of fun writing this. My first fanfiction! This took me like, two weeks, and God knows that there'll still be mistakes here...lol.**

 **I decided to include Jack in here just cause! Swampert is one of my favourite Mega Evolutions and I wanted him to be here somehow!**

 **Read and review please! Especially the latter, as reviews, positive or critical, will always brighten up my day.**

 **-Culius Jaesar**


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